From: Rainer M Krug <Rainer@krugs.de>
To: emacs-orgmode@gnu.org
Cc: schulte.eric@gmail.com
Subject: [babel][PATCHES] ob-R patches for review
Date: Tue, 29 Apr 2014 14:43:29 +0200 [thread overview]
Message-ID: <m2fvkw9uha.fsf@krugs.de> (raw)
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Hi
Attached please find seven patches for review to implement the storing
of org variables in their own environment and to make the org-issued R
code look nicer in the R session.
Thanks,
Rainer
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa
Tel : +33 - (0)9 53 10 27 44
Cell: +33 - (0)6 85 62 59 98
Fax : +33 - (0)9 58 10 27 44
Fax (D): +49 - (0)3 21 21 25 22 44
email: Rainer@krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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[-- Attachment #1.2: 0001-ob-R.el-Write-org-variables-into-own-R-environment.patch --]
[-- Type: text/x-patch, Size: 3528 bytes --]
From b1199e03758f42fde2f75f02a4c18cd71fac5a03 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Thu, 20 Mar 2014 11:35:44 +0100
Subject: [PATCH 1/8] ob-R.el: Write org variables into own R environment
* lisp/ob-R.el (org-babel-expand-body:R): Create empty environment
called `org' in R before adding variables and afterwards lock it and
add it to the R search path.
(org-babel-variable-assignments:R): Assign variables into own
`org' environment in R instead of .GlobalEnv
These patch implements the writing of org variables into a separate R
environment and attaches it to the search path. For the usage of these
variables, nothing changes in R, but:
1) The org variables are now grouped and can be seen via `ls(org)' in
R and are not shown anymore in the .GlobalEnv when using `ls()'
2) As the environment `org' and all bindings are locked, the variables
can not be accidentally deleted. They can be overwritten, but they can
be restored by simply deleting the variable in R or by using
`org$VARIABLE' instead of `VARIABLE'
3) All variables can be saved by simply calling `save(org, FILENAME'
in R which makes it possible to store all variable definitions for
tangling in one file.
---
lisp/ob-R.el | 25 +++++++++----------------
1 file changed, 9 insertions(+), 16 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 62aa7f2..82971de 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -103,8 +103,12 @@ this variable.")
(append
(when (cdr (assoc :prologue params))
(list (cdr (assoc :prologue params))))
- (org-babel-variable-assignments:R params)
- (list body)
+ '("try(detach(org), silent=TRUE)")
+ '("org <- new.env()")
+ (org-babel-variable-assignments:R params)
+ '("lockEnvironment(org)")
+ '("attach(org)")
+ (list body)
(when (cdr (assoc :epilogue params))
(list (cdr (assoc :epilogue params)))))))
(if graphics-file
@@ -203,20 +207,9 @@ This function is called by `org-babel-execute-src-block'."
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE)" name file header row-names)
- (format "%s <- read.table(\"%s\",
- header=%s,
- row.names=%s,
- sep=\"\\t\",
- as.is=TRUE,
- fill=TRUE,
- col.names = paste(\"V\", seq_len(%d), sep =\"\"))"
- name file header row-names max))))
- (format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = org ); lockBinding('%s', org)" name file header row-names name)
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = org ); lockBinding('%s', org)" name file header row-names max name))))
+ (format "assign('%s', %s, envir = org); lockBinding('%s', org)" name (org-babel-R-quote-tsv-field value) name)))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
--
1.8.5.2 (Apple Git-48)
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[-- Attachment #1.3: 0002-Add-saving-of-org-variable-document.patch --]
[-- Type: text/x-patch, Size: 874 bytes --]
From 9b1aed4c855fd54caa7b91e316b26ef7a813b7b0 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Wed, 26 Mar 2014 16:53:29 +0100
Subject: [PATCH 2/8] Add saving of org variable document
* lisp/ob-R.el (org-babel-expand-body:R): add R command to save `org'
environment after variables are stored and locked.
---
lisp/ob-R.el | 1 +
1 file changed, 1 insertion(+)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 82971de..af90e68 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -108,6 +108,7 @@ this variable.")
(org-babel-variable-assignments:R params)
'("lockEnvironment(org)")
'("attach(org)")
+ '("save(org, file='orgVARIABLES.RData')")
(list body)
(when (cdr (assoc :epilogue params))
(list (cdr (assoc :epilogue params)))))))
--
1.8.5.2 (Apple Git-48)
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[-- Attachment #1.4: 0003-Change-R-environment-name-from-org-to-org_variables_.patch --]
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From 27a9daaf3b94c23b437d55c5d1e3d282139ced22 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Wed, 26 Mar 2014 17:09:15 +0100
Subject: [PATCH 3/8] Change R environment name from org to org_variables_
---
lisp/ob-R.el | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index af90e68..b51e582 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -103,12 +103,12 @@ this variable.")
(append
(when (cdr (assoc :prologue params))
(list (cdr (assoc :prologue params))))
- '("try(detach(org), silent=TRUE)")
- '("org <- new.env()")
+ '("try(detach(org_variables_), silent=TRUE)")
+ '("org_variables_ <- new.env()")
(org-babel-variable-assignments:R params)
- '("lockEnvironment(org)")
- '("attach(org)")
- '("save(org, file='orgVARIABLES.RData')")
+ '("lockEnvironment(org_variables_)")
+ '("attach(org_variables_)")
+ '("save(org_variables_, file='org_variables.RData')")
(list body)
(when (cdr (assoc :epilogue params))
(list (cdr (assoc :epilogue params)))))))
@@ -208,9 +208,9 @@ This function is called by `org-babel-execute-src-block'."
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = org ); lockBinding('%s', org)" name file header row-names name)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = org ); lockBinding('%s', org)" name file header row-names max name))))
- (format "assign('%s', %s, envir = org); lockBinding('%s', org)" name (org-babel-R-quote-tsv-field value) name)))
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = org_variables_ ); lockBinding('%s', org_variables_)" name file header row-names name)
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = org_variables_ ); lockBinding('%s', org_variables_)" name file header row-names max name))))
+ (format "assign('%s', %s, envir = org_variables_); lockBinding('%s', org_variables_)" name (org-babel-R-quote-tsv-field value) name)))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
--
1.8.5.2 (Apple Git-48)
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[-- Attachment #1.5: 0004-Rename-org_variables-to-.org_variables.patch --]
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From e8c977e0b38eb7eb64ed29f55bd985ca2e135c4c Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Fri, 28 Mar 2014 12:13:53 +0100
Subject: [PATCH 4/8] Rename `org_variables' to `.org_variables'
* lisp/ob-R.el (org-babel-R-assign-elisp, org-babel-expand-body:R):
Change name of R environment from `org_variables' to
`.org_variables'. The `.' makes the environment hidden in R and it
can not be directly deleted in R by using `rm(list=ls()'
---
lisp/ob-R.el | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index b51e582..214c14d 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -103,12 +103,12 @@ this variable.")
(append
(when (cdr (assoc :prologue params))
(list (cdr (assoc :prologue params))))
- '("try(detach(org_variables_), silent=TRUE)")
- '("org_variables_ <- new.env()")
+ '("try(detach(.org_variables_), silent=TRUE)")
+ '(".org_variables_ <- new.env()")
(org-babel-variable-assignments:R params)
- '("lockEnvironment(org_variables_)")
- '("attach(org_variables_)")
- '("save(org_variables_, file='org_variables.RData')")
+ '("lockEnvironment(.org_variables_)")
+ '("attach(.org_variables_)")
+ '("save(.org_variables_, file='org_variables.RData')")
(list body)
(when (cdr (assoc :epilogue params))
(list (cdr (assoc :epilogue params)))))))
@@ -208,9 +208,9 @@ This function is called by `org-babel-execute-src-block'."
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = org_variables_ ); lockBinding('%s', org_variables_)" name file header row-names name)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = org_variables_ ); lockBinding('%s', org_variables_)" name file header row-names max name))))
- (format "assign('%s', %s, envir = org_variables_); lockBinding('%s', org_variables_)" name (org-babel-R-quote-tsv-field value) name)))
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names name)
+ (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names max name))))
+ (format "assign('%s', %s, envir = .org_variables_); lockBinding('%s', .org_variables_)" name (org-babel-R-quote-tsv-field value) name)))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
--
1.8.5.2 (Apple Git-48)
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[-- Attachment #1.6: 0005-Adds-visual-separators.patch --]
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From ba532e45ba7fe373effbeef3781e744b33f532a4 Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Mon, 31 Mar 2014 16:57:14 +0200
Subject: [PATCH 5/8] Adds visual separators
* ob-R.el (org-babel-expand-body:R): Add visual separators in R code
to separate the automatically added code from the code from the code blocks.
---
lisp/ob-R.el | 4 ++++
1 file changed, 4 insertions(+)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 214c14d..3534580 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -103,12 +103,16 @@ this variable.")
(append
(when (cdr (assoc :prologue params))
(list (cdr (assoc :prologue params))))
+ '("######################################################################")
+ '("## Beginning org variable transfer")
'("try(detach(.org_variables_), silent=TRUE)")
'(".org_variables_ <- new.env()")
(org-babel-variable-assignments:R params)
'("lockEnvironment(.org_variables_)")
'("attach(.org_variables_)")
'("save(.org_variables_, file='org_variables.RData')")
+ '("## end org variable transfer")
+ '("######################################################################")
(list body)
(when (cdr (assoc :epilogue params))
(list (cdr (assoc :epilogue params)))))))
--
1.8.5.2 (Apple Git-48)
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[-- Attachment #1.7: 0006-Make-R-code-look-nicer-in-R.patch --]
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From b3ddb3bf0bb327187acdd898a6173d22ceefe5fb Mon Sep 17 00:00:00 2001
From: "Rainer M. Krug" <R.M.Krug@gmail.com>
Date: Mon, 7 Apr 2014 10:52:00 +0200
Subject: [PATCH 6/8] Make R code look nicer in R
* lisp/ob-R.el (org-babel-expand-body:R): Added Space to the R code
blocks to make them easier identifiable in R.
---
lisp/ob-R.el | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/lisp/ob-R.el b/lisp/ob-R.el
index 3534580..5edbed9 100644
--- a/lisp/ob-R.el
+++ b/lisp/ob-R.el
@@ -105,12 +105,12 @@ this variable.")
(list (cdr (assoc :prologue params))))
'("######################################################################")
'("## Beginning org variable transfer")
- '("try(detach(.org_variables_), silent=TRUE)")
- '(".org_variables_ <- new.env()")
+ '(" try(detach(.org_variables_), silent=TRUE)")
+ '(" .org_variables_ <- new.env()")
(org-babel-variable-assignments:R params)
- '("lockEnvironment(.org_variables_)")
- '("attach(.org_variables_)")
- '("save(.org_variables_, file='org_variables.RData')")
+ '(" lockEnvironment(.org_variables_)")
+ '(" attach(.org_variables_)")
+ '(" save(.org_variables_, file='org_variables.RData')")
'("## end org variable transfer")
'("######################################################################")
(list body)
@@ -212,9 +212,9 @@ This function is called by `org-babel-execute-src-block'."
"TRUE" "FALSE"))
(row-names (if rownames-p "1" "NULL")))
(if (= max min)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names name)
- (format "assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names max name))))
- (format "assign('%s', %s, envir = .org_variables_); lockBinding('%s', .org_variables_)" name (org-babel-R-quote-tsv-field value) name)))
+ (format " assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names name)
+ (format " assign( '%s', read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE, fill=TRUE, col.names = paste(\"V\", seq_len(%d), sep =\"\") ), envir = .org_variables_ ); lockBinding('%s', .org_variables_)" name file header row-names max name))))
+ (format " assign('%s', %s, envir = .org_variables_); lockBinding('%s', .org_variables_)" name (org-babel-R-quote-tsv-field value) name)))
(defvar ess-ask-for-ess-directory) ; dynamically scoped
(defun org-babel-R-initiate-session (session params)
--
1.8.5.2 (Apple Git-48)
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next reply other threads:[~2014-04-29 12:45 UTC|newest]
Thread overview: 24+ messages / expand[flat|nested] mbox.gz Atom feed top
2014-04-29 12:43 Rainer M Krug [this message]
2014-04-29 18:15 ` [babel][PATCHES] ob-R patches for review Charles Berry
2014-04-30 12:28 ` Rainer M Krug
2014-04-30 22:49 ` Charles C. Berry
2014-05-01 9:10 ` Rainer M Krug
2014-05-07 10:27 ` Eric Schulte
2014-05-08 2:26 ` Charles Berry
2014-05-08 10:02 ` Rainer M Krug
2014-05-09 9:11 ` Rainer M Krug
2014-05-09 12:02 ` Rainer M Krug
2014-05-08 9:57 ` Rainer M Krug
2014-05-09 13:03 ` Bastien
2014-05-09 13:45 ` Rainer M Krug
2014-05-09 14:34 ` Eric Schulte
2014-05-12 8:33 ` Rainer M Krug
2014-05-12 12:23 ` Suvayu Ali
2014-05-12 12:41 ` Rainer M Krug
2014-05-12 14:01 ` Queestion concerning lists - was: " Rainer M Krug
2014-05-12 15:23 ` Eric Schulte
2014-05-12 15:21 ` Eric Schulte
2014-05-12 19:08 ` Rainer M Krug
2014-05-12 22:05 ` Charles C. Berry
[not found] ` <m2y4y2f499.fsf@krugs.de>
2014-05-16 18:22 ` Charles C. Berry
2014-06-06 16:11 ` Eric Schulte
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